how two join and arrange two files together

amrita at iisermohali.ac.in amrita at iisermohali.ac.in
Thu Jul 23 16:34:15 CEST 2009


I tried to print those lines having C value missing by:

import re
expr = re.compile("C = None")
f = open("/home/amrita/helix.dat")
for line in f:
    if expr.search(line):
       print line

but it is not giving any value.

>
> Hi,
>
> I have two large files:
>
> FileA
> 15 ALA H = 8.05	N = 119.31 CA = 52.18 HA = 4.52	C =
> 21 ALA H = 7.66	N = 123.58 CA = 54.33 HA = C = 179.35
> 23 ALA H = 8.78	N =  CA =  HA = C = 179.93.................
>
> and
>
> FileB
> 21 ALA  helix (helix_alpha, helix2)
> 23 ALA  helix (helix_alpha, helix3)
> 38 ALA  helix (helix_alpha, helix3)...........
>
> now what i want that i will make another file in which i will join the two
> file in such a way that only matching entries will come like here 21 and
> 23 ALA is in both files, so the output will be something like:-
>
> 21 ALA H = 7.66	N = 123.58 CA = 54.33 HA = C = 179.35| 21 ALA  helix
> (helix_alpha, helix2)
> 23 ALA H = 8.78	N =  CA =  HA = C = 179.93|23 ALA  helix (helix_alpha,
> helix3)
>
> and further i will make another file in which i will be able to put those
> lines form this file based on the missing atom value, like for 21 ALA HA
> is not defined so i will put it another file based on its HA missing value
> similarly i will put 23 ALA on another file based on its missing N,CA and
> HA value.
>
> I tried to join the two file based on their matching entries by:---
>>>>from collections import defaultdict
>>>>
>>>> if __name__ == "__main__":
> ...      a = open("/home/amrita/alachems/chem100.txt")
> ...      c = open("/home/amrita/secstr/secstr100.txt")
> ...
>>>> def source(stream):
> ...     return (line.strip() for line in stream)
> ...
> ...
>>>> def merge(sources):
> ...     for m in merge([source(a),source(c)]):
> ...         print "|".join(c.ljust(10) for c in m)
> ...
>
> but it is not giving any value.
>
>
>
>
>
>
> Thanks,
> Amrita Kumari
> Research Fellow
> IISER Mohali
> Chandigarh
> INDIA
>


Amrita Kumari
Research Fellow
IISER Mohali
Chandigarh
INDIA




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